remotes::install_github('al-obrien/pangoRo'){pangoRo}
Peace of mind with PANGO Lineages
Allen O’Brien
Principal Data Scientist @ PHSA DARE
2023-08-30
Applied Epi Community
PANGO Lineages
- Track spread of COVID-19 transmission
- Document & classify lineages
- Cluster of sequences associated with epidemiological event ref
Aliases
Short Name
BA.1
EG.1
Long Name
B.1.1.529.1
XBB.1.9.2.1
[BJ.1, BM.1.1.1]
BJ.1 → B.1.1.529.2.10.1.1
BM.1.1.1 → B.1.1.529.2.75.3.1.1.1
Alias struggles
- String format, requires parsing
- Hierarchical relationship
- Countless strains
- Many of the tools are coded in Python NextStrain Project
Install & Load {pangoRo}
Based upon the Python package pango_aliasor.
Install the package from GitHub…
Load into session…
Accessing reference tables
| alias | lineage | recomb |
|---|---|---|
| A | FALSE | |
| B | FALSE | |
| C | B.1.1.1 | FALSE |
| D | B.1.1.25 | FALSE |
| G | B.1.258.2 | FALSE |
| K | B.1.1.277 | FALSE |
| L | B.1.1.10 | FALSE |
| M | B.1.1.294 | FALSE |
| N | B.1.1.33 | FALSE |
| P | B.1.1.28 | FALSE |
| Q | B.1.1.7 | FALSE |
| R | B.1.1.316 | FALSE |
| S | B.1.1.217 | FALSE |
| U | B.1.177.60 | FALSE |
| V | B.1.177.54 | FALSE |
| W | B.1.177.53 | FALSE |
| Y | B.1.177.52 | FALSE |
| Z | B.1.177.50 | FALSE |
| AA | B.1.177.15 | FALSE |
| AB | B.1.160.16 | FALSE |
| AC | B.1.1.405 | FALSE |
| AD | B.1.1.315 | FALSE |
| AE | B.1.1.306 | FALSE |
| AF | B.1.1.305 | FALSE |
| AG | B.1.1.297 | FALSE |
| AH | B.1.1.241 | FALSE |
| AJ | B.1.1.240 | FALSE |
| AK | B.1.1.232 | FALSE |
| AL | B.1.1.231 | FALSE |
| AM | B.1.1.216 | FALSE |
| AN | B.1.1.200 | FALSE |
| AP | B.1.1.70 | FALSE |
| AQ | B.1.1.39 | FALSE |
| AS | B.1.1.317 | FALSE |
| AT | B.1.1.370 | FALSE |
| AU | B.1.466.2 | FALSE |
| AV | B.1.1.482 | FALSE |
| AW | B.1.1.464 | FALSE |
| AY | B.1.617.2 | FALSE |
| AZ | B.1.1.318 | FALSE |
| BA | B.1.1.529 | FALSE |
| BB | B.1.621.1 | FALSE |
| BC | B.1.1.529.1.1.1 | FALSE |
| BD | B.1.1.529.1.17.2 | FALSE |
| BE | B.1.1.529.5.3.1 | FALSE |
| BF | B.1.1.529.5.2.1 | FALSE |
| BG | B.1.1.529.2.12.1 | FALSE |
| BH | B.1.1.529.2.38.3 | FALSE |
| BJ | B.1.1.529.2.10.1 | FALSE |
| BK | B.1.1.529.5.1.10 | FALSE |
| BL | B.1.1.529.2.75.1 | FALSE |
| BM | B.1.1.529.2.75.3 | FALSE |
| BN | B.1.1.529.2.75.5 | FALSE |
| BP | B.1.1.529.2.3.16 | FALSE |
| BQ | B.1.1.529.5.3.1.1.1.1 | FALSE |
| BR | B.1.1.529.2.75.4 | FALSE |
| BS | B.1.1.529.2.3.2 | FALSE |
| BT | B.1.1.529.5.1.21 | FALSE |
| BU | B.1.1.529.5.2.16 | FALSE |
| BV | B.1.1.529.5.2.20 | FALSE |
| BW | B.1.1.529.5.6.2 | FALSE |
| BY | B.1.1.529.2.75.6 | FALSE |
| BZ | B.1.1.529.5.2.3 | FALSE |
| CA | B.1.1.529.2.75.2 | FALSE |
| CB | B.1.1.529.2.75.9 | FALSE |
| CC | B.1.1.529.5.3.1.1.1.2 | FALSE |
| CD | B.1.1.529.5.2.31 | FALSE |
| CE | B.1.1.529.5.2.33 | FALSE |
| CF | B.1.1.529.5.2.27 | FALSE |
| CG | B.1.1.529.5.2.26 | FALSE |
| CH | B.1.1.529.2.75.3.4.1.1 | FALSE |
| CJ | B.1.1.529.2.75.3.1.1.1 | FALSE |
| CK | B.1.1.529.5.2.24 | FALSE |
| CL | B.1.1.529.5.1.29 | FALSE |
| CM | B.1.1.529.2.3.20 | FALSE |
| CN | B.1.1.529.5.2.21 | FALSE |
| CP | B.1.1.529.5.2.6 | FALSE |
| CQ | B.1.1.529.5.3.1.4.1.1 | FALSE |
| CR | B.1.1.529.5.2.18 | FALSE |
| CS | B.1.1.529.4.1.10 | FALSE |
| CT | B.1.1.529.5.2.36 | FALSE |
| CU | B.1.1.529.5.1.26 | FALSE |
| CV | B.1.1.529.2.75.3.1.1.3 | FALSE |
| CW | B.1.1.529.5.3.1.1.1.1.1.1.14 | FALSE |
| CY | B.1.1.529.5.2.7 | FALSE |
| CZ | B.1.1.529.5.3.1.1.1.1.1.1.1 | FALSE |
| DA | B.1.1.529.5.2.38 | FALSE |
| DB | B.1.1.529.5.2.25 | FALSE |
| DC | B.1.1.529.4.6.5 | FALSE |
| DD | B.1.1.529.2.3.21 | FALSE |
| DE | B.1.1.529.5.1.23 | FALSE |
| DF | B.1.1.529.5.10.1 | FALSE |
| DG | B.1.1.529.5.2.24.2.1.1 | FALSE |
| DH | B.1.1.529.5.1.22 | FALSE |
| DJ | B.1.1.529.5.1.25 | FALSE |
| DK | B.1.1.529.5.3.1.1.1.1.1.1.7 | FALSE |
| DL | B.1.1.529.5.1.15 | FALSE |
| DM | B.1.1.529.5.3.1.1.1.1.1.1.15 | FALSE |
| DN | B.1.1.529.5.3.1.1.1.1.1.1.5 | FALSE |
| DP | B.1.1.529.5.3.1.1.1.1.1.1.8 | FALSE |
| Lineage | Most common countries | Earliest date | # designated | # assigned | Description | WHO Name | full_name |
|---|---|---|---|---|---|---|---|
| A.5 | Spain 62.0%, United Kingdom 14.0%, Uruguay 5.0%, Portugal 2.0%, Peru 2.0% | 2020-03-01 | 439 | 525 | A lineage with a lot of representation from Spanish-speaking countries. A Spanish/ South-American lineage, but now with sequences from an outbreak in Scotland. Also now includes what was previously A.10. | NA | NA |
| B | United States of America 40.0%, United Kingdom 15.0%, China 7.0%, Mexico 5.0%, Germany 3.0% | 2019-12-24 | 4001 | 10237 | One of the two original haplotypes of the pandemic(and first to be discovered) | NA | NA |
| B.1 | United States of America 46.0%, Turkey 11.0%, United Kingdom 6.0%, Canada 4.0%, France 3.0% | 2020-01-01 | 46228 | 118909 | A large European lineage the origin of which roughly corresponds to the Northern Italian outbreak early in 2020. | NA | NA |
| B.1.1 | United Kingdom 26.0%, United States of America 16.0%, Japan 6.0%, Russia 6.0%, Turkey 5.0% | 2020-02-03 | 22790 | 51415 | European lineage with 3 clear SNPs `28881GA`,`28882GA`,`28883GC` | NA | NA |
| B.1.1.7 | United Kingdom 23.0%, United States of America 20.0%, Germany 9.0%, Sweden 6.0%, Denmark 6.0% | 2020-02-07 | 69636 | 1115159 | UK lineage of concern, associated with the N501Y mutation. More information can be found at cov-lineages.org/global_report.html | NA | NA |
| B.1.1.28 | Brazil 79.0%, Philippines 9.0%, United States of America 4.0%, Paraguay 2.0%, Japan 1.0% | 2020-02-10 | 854 | 5071 | Brazil mostly, absorbed B.1.1.94 and B.1.1.143 | NA | NA |
| P.1 | Brazil 58.0%, United States of America 26.0%, Chile 3.0%, Argentina 1.0%, Spain 1.0% | 2020-04-07 | 29946 | 72579 | Alias of B.1.1.28.1, Brazilian lineage with a number of spike mutations with likely functional significance E484K, K417T, and N501Y. Described in https://virological.org/t/genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-manaus-preliminary-findings/586. From #77 | NA | B.1.1.28.1 |
| B.1.1.50 | Israel 88.0%, Palestine 5.0%, United Kingdom 4.0%, Denmark 1.0%, United States of America 0.0% | 2020-03-29 | 461 | 1464 | Israel and Palestine | NA | NA |
| B.1.1.529 | United States of America 35.0%, Germany 13.0%, India 9.0%, Turkey 5.0%, Russia 5.0% | 2020-04-14 | 0 | 8043 | South Africa and Botswana lineage, from pango-designation issue #343 | NA | NA |
| BA.1 | United Kingdom 41.0%, United States of America 22.0%, Denmark 5.0%, Germany 4.0%, Brazil 4.0% | 2020-06-25 | 66001 | 423104 | Alias of B.1.1.529.1, from pango-designation issue #361 | NA | B.1.1.529.1 |
| BA.1.1 | United States of America 47.0%, United Kingdom 19.0%, Germany 7.0%, Canada 4.0%, France 2.0% | 2020-01-27 | 104527 | 965459 | Alias of B.1.1.529.1.1, from pango-designation issue #360 | NA | B.1.1.529.1.1 |
| BA.1.1.14 | United Kingdom 51.0%, United States of America 16.0%, Germany 6.0%, Spain 6.0%, Brazil 4.0% | 2020-12-10 | 6372 | 19706 | Alias of B.1.1.529.1.1.14, European lineage | NA | B.1.1.529.1.1.14 |
| BA.1.15 | United States of America 69.0%, United Kingdom 13.0%, Canada 3.0%, Germany 2.0%, Brazil 2.0% | 2020-06-14 | 35340 | 181922 | Alias of B.1.1.529.1.15, lineage in USA and other countries | NA | B.1.1.529.1.15 |
| BA.1.17 | Australia 27.0%, Spain 16.0%, United Kingdom 13.0%, United States of America 8.0%, Germany 6.0% | 2020-11-06 | 11367 | 72251 | Alias of B.1.1.529.1.17, European lineage | NA | B.1.1.529.1.17 |
| BA.1.17.2 | United Kingdom 67.0%, United States of America 6.0%, Canada 4.0%, Germany 4.0%, Denmark 3.0% | 2020-10-23 | 29853 | 192714 | Alias of B.1.1.529.1.17.2, lineage from pango-designation issue #462 | NA | B.1.1.529.1.17.2 |
| BA.1.21 | Norway 47.0%, Germany 9.0%, Italy 5.0%, South_Africa 5.0%, Denmark 5.0% | 2021-01-09 | 4525 | 6914 | Alias of B.1.1.529.1.21, lineage from pango-designation issue #505 | NA | B.1.1.529.1.21 |
| BA.2 | United Kingdom 29.0%, Germany 13.0%, Denmark 11.0%, United States of America 11.0%, France 7.0% | 2020-03-28 | 111257 | 1187286 | Alias of B.1.1.529.2, from pango-designation issue #361 | NA | B.1.1.529.2 |
| BA.2.3 | United States of America 25.0%, United Kingdom 17.0%, Canada 9.0%, Japan 8.0%, South_Korea 6.0% | 2020-09-24 | 19173 | 108564 | Alias of B.1.1.529.2.3, lineage in Philippines and other countries | NA | B.1.1.529.2.3 |
| BA.2.3.2 | Vietnam 29.0%, Japan 26.0%, United States of America 11.0%, Australia 6.0%, Laos 4.0% | 2022-01-22 | 618 | 2239 | Alias of B.1.1.529.2.3.2, Vietnam and Japan lineage | NA | B.1.1.529.2.3.2 |
| BS.1.1 | Japan 45.0%, Australia 16.0%, Vietnam 11.0%, South_Korea 7.0%, Denmark 4.0% | 2022-08-20 | 13 | 461 | Alias of B.1.1.529.2.3.2.1.1, Vietnam lineage, defined by S:K356T, from pango-designation issue #1097 | NA | B.1.1.529.2.3.2.1.1 |
| CM.2.1 | Australia 47.0%, Indonesia 27.0%, Singapore 5.0%, South_Korea 5.0%, Germany 5.0% | 2022-10-30 | 7 | 60 | Alias of B.1.1.529.2.3.20.2.1, Indonesia/Australia, S:F486S, issue #1356 | NA | B.1.1.529.2.3.20.2.1 |
| CM.4.1 | Japan 63.0%, Philippines 20.0%, United States of America 12.0%, Canada 1.0%, New_Zealand 1.0% | 2022-09-25 | 36 | 203 | Alias of B.1.1.529.2.3.20.4.1, S:K478R, Philippines/Japan/USA | NA | B.1.1.529.2.3.20.4.1 |
| CM.7.1.1 | France 42.0%, Spain 25.0%, Italy 25.0%, Israel 8.0% | 2023-03-22 | 15 | 12 | Alias of B.1.1.529.2.3.20.7.1, S:R403K, Europe, from sars-cov-2-variants/lineage-proposals#37 | NA | B.1.1.529.2.3.20.7.1 |
| CM.8.1 | United States of America 40.0%, Philippines 15.0%, Canada 14.0%, Japan 8.0%, South_Korea 6.0% | 2022-10-16 | 248 | 1110 | Alias of B.1.1.529.2.3.20.8.1, Australia/England, S:F486S | NA | B.1.1.529.2.3.20.8.1 |
| CM.8.1.1 | Singapore 86.0%, South_Korea 4.0%, Japan 3.0%, Malaysia 3.0%, Germany 1.0% | 2022-12-12 | 24 | 90 | Alias of B.1.1.529.2.3.20.8.1.1, Singapore/Malaysia, S:K147N | NA | B.1.1.529.2.3.20.8.1.1 |
| FV.1 | Japan 42.0%, South_Korea 22.0%, Philippines 10.0%, United States of America 6.0%, Dominican_Republic 4.0% | 2023-01-29 | 11 | 200 | Alias of B.1.1.529.2.3.20.8.1.1.1, S:R346T, M:E11Q, Singapore/SouthKorea/Japan/Philippines/HK | NA | B.1.1.529.2.3.20.8.1.1.1 |
| CM.8.1.2 | United States of America 23.0%, Germany 23.0%, Japan 14.0%, South_Korea 11.0%, China 6.0% | 2022-12-15 | 15 | 35 | Alias of B.1.1.529.2.3.20.8.1.2, Germany/USA, S:K147I | NA | B.1.1.529.2.3.20.8.1.2 |
| CM.8.1.5 | Philippines 94.0%, Japan 3.0%, Australia 3.0% | 2023-01-10 | 26 | 36 | Alias of B.1.1.529.2.3.20.8.1.5, S:K150E, S:Y248H, N:A155V, Philippines, from sars-cov-2-variants/lineage-proposals#293 | NA | B.1.1.529.2.3.20.8.1.5 |
| CM.10 | Philippines 41.0%, United States of America 23.0%, Indonesia 10.0%, South_Korea 7.0%, Japan 4.0% | 2022-11-01 | 36 | 283 | Alias of B.1.1.529.2.3.20.10, USA/South Korea/Singapore, S:K478T reversion, S:V445A | NA | B.1.1.529.2.3.20.10 |
| BA.2.3.21 | Philippines 39.0%, United States of America 28.0%, Indonesia 17.0%, Vietnam 11.0%, Thailand 6.0% | 2022-02-16 | 9 | 18 | Alias of B.1.1.529.2.3.21, Philippines, S:P9L and 493 reversion | NA | B.1.1.529.2.3.21 |
| BA.2.9 | Denmark 25.0%, Germany 17.0%, United Kingdom 13.0%, United States of America 10.0%, Sweden 5.0% | 2020-07-21 | 42851 | 207832 | Alias of B.1.1.529.2.9, European lineage, from pango-designation issue #432 | NA | B.1.1.529.2.9 |
| BA.2.10.1 | Australia 24.0%, India 15.0%, United States of America 12.0%, United Kingdom 12.0%, Japan 8.0% | 2021-12-23 | 1668 | 8605 | Alias of B.1.1.529.2.10.1, lineage in Singapore and other countries | NA | B.1.1.529.2.10.1 |
| BA.2.12.1 | United States of America 82.0%, Canada 5.0%, United Kingdom 2.0%, Germany 1.0%, Mexico 1.0% | 2020-04-15 | 39747 | 275603 | Alias of B.1.1.529.2.12.1, USA and Canada lineage, from pango-designation issue #499 | NA | B.1.1.529.2.12.1 |
| BA.2.13 | United States of America 37.0%, Belgium 20.0%, Finland 6.0%, Germany 5.0%, Netherlands 3.0% | 2022-01-01 | 1245 | 5484 | Alias of B.1.1.529.2.13, Europe lineage, from pango-designation issue #531 | NA | B.1.1.529.2.13 |
| BA.2.23 | United Kingdom 76.0%, United States of America 7.0%, Brazil 3.0%, Germany 2.0%, France 2.0% | 2020-10-11 | 6280 | 16676 | Alias of B.1.1.529.2.23, UK lineage, from pango-designation issue #546 | NA | B.1.1.529.2.23 |
| BA.2.36 | Germany 21.0%, France 14.0%, Belgium 14.0%, United Kingdom 13.0%, United States of America 8.0% | 2021-11-15 | 3000 | 11475 | Alias of B.1.1.529.2.36, mainly found in Germany, Belgium, England and Denmark, from pango-designation issue #565 | NA | B.1.1.529.2.36 |
| BA.2.56 | Japan 16.0%, Brazil 14.0%, Spain 10.0%, Germany 9.0%, United States of America 9.0% | 2020-06-16 | 496 | 6992 | Alias of B.1.1.529.2.56, mainly found in Europe, from pango-designation issue #668 | NA | B.1.1.529.2.56 |
| BA.2.65 | United States of America 23.0%, Canada 16.0%, Japan 12.0%, Sweden 9.0%, Germany 9.0% | 2021-10-11 | 2022 | 7422 | Alias of B.1.1.529.2.65, Canada and USA lineage | NA | B.1.1.529.2.65 |
| BA.2.75 | India 67.0%, United States of America 5.0%, Canada 4.0%, Australia 3.0%, Japan 2.0% | 2020-08-08 | 565 | 4439 | Alias of B.1.1.529.2.75, mainly found in India, from pango-designation issue #773 | NA | B.1.1.529.2.75 |
| BL.1 | India 28.0%, United States of America 9.0%, United Kingdom 7.0%, Japan 7.0%, Australia 6.0% | 2022-01-03 | 26 | 2041 | Alias of B.1.1.529.2.75.1.1, mainly found in India from pango-designation issue #944, S:R346T on polytomy | NA | B.1.1.529.2.75.1.1 |
| BA.2.75.2 | India 21.0%, United States of America 17.0%, United Kingdom 9.0%, Australia 8.0%, Canada 5.0% | 2022-01-01 | 1500 | 5043 | Alias of B.1.1.529.2.75.2, mainly found in Asia and Australia, pango-designation issue #963 | NA | B.1.1.529.2.75.2 |
| BM.1.1.1 | India 32.0%, United States of America 12.0%, Singapore 11.0%, Australia 5.0%, South_Korea 4.0% | 2022-07-12 | 224 | 389 | Alias of B.1.1.529.2.75.3.1.1.1, mainly found in India (West Bengal), defined by S:490S From #1043 | NA | B.1.1.529.2.75.3.1.1.1 |
| CJ.1.1 | Singapore 32.0%, Malaysia 18.0%, United Kingdom 14.0%, Japan 11.0%, Canada 6.0% | 2022-10-12 | 11 | 124 | Alias of B.1.1.529.2.75.3.1.1.1.1.1, S:V445A, Singapore/Malaysia/Japan, from issue #1384 | NA | B.1.1.529.2.75.3.1.1.1.1.1 |
| CJ.1.3 | South_Korea 82.0%, Japan 7.0%, Austria 6.0%, Canada 1.0%, Germany 1.0% | 2022-11-03 | 245 | 1295 | Alias of B.1.1.529.2.75.3.1.1.1.1.3, A261G reversion, G4960A, C14790T, South Korea | NA | B.1.1.529.2.75.3.1.1.1.1.3 |
| CJ.1.3.1 | Japan 80.0%, South_Korea 18.0%, China 2.0% | 2023-03-17 | 48 | 88 | Alias of B.1.1.529.2.75.3.1.1.1.1.3.1, S:R214S, ORF1a:G3578S, South Korea/Japan, sars-cov-2-variants/lineage-proposals#287 | NA | B.1.1.529.2.75.3.1.1.1.1.3.1 |
| CJ.1.3.2 | South_Korea 97.0%, Singapore 2.0%, Japan 1.0%, United States of America 1.0% | 2022-11-13 | 198 | 196 | Alias of B.1.1.529.2.75.3.1.1.1.1.3.2, S:D936H, South Korea, sars-cov-2-variants/lineage-proposals#287 | NA | B.1.1.529.2.75.3.1.1.1.1.3.2 |
| EP.1 | Bhutan 39.0%, Canada 15.0%, Singapore 15.0%, Australia 9.0%, Japan 4.0% | 2022-12-12 | 12 | 46 | Alias of B.1.1.529.2.75.3.1.1.4.1, S:L452R, Bhutan, from #1676 | NA | B.1.1.529.2.75.3.1.1.4.1 |
| EP.2 | France 41.0%, Belgium 30.0%, Germany 17.0%, Austria 4.0%, United States of America 4.0% | 2022-11-15 | 33 | 46 | Alias of B.1.1.529.2.75.3.1.1.4.2, S:S1147L, N:G212S, Belgium/Europe | NA | B.1.1.529.2.75.3.1.1.4.2 |
| BM.4.1.1 | United States of America 24.0%, India 22.0%, United Kingdom 11.0%, Australia 6.0%, Singapore 4.0% | 2022-07-20 | 35 | 917 | Alias of B.1.1.529.2.75.3.4.1.1, mainly found in India, defined by S:346T | NA | B.1.1.529.2.75.3.4.1.1 |
| CH.1.1 | United Kingdom 27.0%, Germany 11.0%, United States of America 9.0%, South_Korea 6.0%, Netherlands 4.0% | 2022-02-10 | 4929 | 19515 | Alias of B.1.1.529.2.75.3.4.1.1.1.1, defined by S:L452R, issue #1113 | NA | B.1.1.529.2.75.3.4.1.1.1.1 |
| CH.1.1.1 | United Kingdom 37.0%, Sweden 14.0%, Australia 9.0%, Germany 5.0%, United States of America 5.0% | 2022-10-15 | 2050 | 6704 | Alias of B.1.1.529.2.75.3.4.1.1.1.1.1, defined by S:N185D | NA | B.1.1.529.2.75.3.4.1.1.1.1.1 |
| DV.1 | United Kingdom 56.0%, United States of America 14.0%, Iceland 14.0%, Sweden 3.0%, Canada 2.0% | 2022-12-05 | 187 | 284 | Alias of B.1.1.529.2.75.3.4.1.1.1.1.1.1, UK, defined by S:L176F | NA | B.1.1.529.2.75.3.4.1.1.1.1.1.1 |
| DV.1.1 | United Kingdom 42.0%, Canada 28.0%, United States of America 5.0%, Germany 4.0%, Australia 4.0% | 2022-11-28 | 582 | 1428 | Alias of B.1.1.529.2.75.3.4.1.1.1.1.1.1.1, defined by S:Q613H and N:T265I, from #1720 | NA | B.1.1.529.2.75.3.4.1.1.1.1.1.1.1 |
| DV.2 | United Kingdom 77.0%, Germany 11.0%, United States of America 3.0%, Austria 3.0%, Canada 1.0% | 2022-11-20 | 71 | 222 | Alias of B.1.1.529.2.75.3.4.1.1.1.1.1.2, UK, defined by S:I569V | NA | B.1.1.529.2.75.3.4.1.1.1.1.1.2 |
| DV.3 | United Kingdom 81.0%, Ireland 3.0%, United States of America 3.0%, Greece 2.0%, Germany 1.0% | 2022-11-11 | 256 | 496 | Alias of B.1.1.529.2.75.3.4.1.1.1.1.1.3, UK, defined by ORF1a:E377K | NA | B.1.1.529.2.75.3.4.1.1.1.1.1.3 |
| DV.3.1 | Portugal 32.0%, United Kingdom 22.0%, Ireland 8.0%, France 7.0%, Germany 6.0% | 2022-11-25 | 49 | 167 | Alias of B.1.1.529.2.75.3.4.1.1.1.1.1.3.1 found mainly in Portugal and UK, from pango-designation issue #1626 | NA | B.1.1.529.2.75.3.4.1.1.1.1.1.3.1 |
| DV.4 | Singapore 38.0%, Japan 23.0%, Malaysia 19.0%, Australia 13.0%, United Kingdom 3.0% | 2022-12-01 | 34 | 222 | Alias of B.1.1.529.2.75.3.4.1.1.1.1.1.4, Malaysia/Singapore, S:I714V, from #1617 | NA | B.1.1.529.2.75.3.4.1.1.1.1.1.4 |
| DV.5 | Australia 51.0%, United Kingdom 19.0%, Finland 17.0%, New_Zealand 4.0%, Italy 2.0% | 2023-01-06 | 38 | 191 | Alias of B.1.1.529.2.75.3.4.1.1.1.1.1.5, England/Australia, ORF1a:R24C, S:613H, from #1753 | NA | B.1.1.529.2.75.3.4.1.1.1.1.1.5 |
| DV.6 | United Kingdom 64.0%, Germany 6.0%, Denmark 3.0%, Spain 3.0%, Finland 3.0% | 2022-11-13 | 1384 | 3544 | Alias of B.1.1.529.2.75.3.4.1.1.1.1.1.6, T15591C | NA | B.1.1.529.2.75.3.4.1.1.1.1.1.6 |
| DV.6.1 | Finland 25.0%, Poland 17.0%, Germany 16.0%, Denmark 8.0%, Austria 8.0% | 2023-01-20 | 116 | 146 | Alias of B.1.1.529.2.75.3.4.1.1.1.1.1.6.1, S:Q613H, T15591C, Central Europe | NA | B.1.1.529.2.75.3.4.1.1.1.1.1.6.1 |
| DV.6.2 | Japan 26.0%, South_Korea 20.0%, United States of America 10.0%, Austria 10.0%, Singapore 5.0% | 2023-02-13 | 145 | 315 | Alias of B.1.1.529.2.75.3.4.1.1.1.1.1.6.2, S:Q613H, C6628T, Asia From #2045 | NA | B.1.1.529.2.75.3.4.1.1.1.1.1.6.2 |
| DV.7 | United Kingdom 69.0%, Germany 8.0%, Canada 6.0%, United States of America 5.0%, Sweden 2.0% | 2023-01-19 | 226 | 264 | Alias of B.1.1.529.2.75.3.4.1.1.1.1.1.7, S:L858I, ORF1a:A3548V, England, from #2038 | NA | B.1.1.529.2.75.3.4.1.1.1.1.1.7 |
| DV.7.1 | Spain 57.0%, Ireland 11.0%, United States of America 11.0%, United Kingdom 7.0%, Israel 6.0% | 2023-05-11 | 73 | 205 | Alias of B.1.1.529.2.75.3.4.1.1.1.1.1.7.1, S:L455F, S:F456L, Spain/Austria, from sars-cov-2-variants/lineage-proposals#135 | NA | B.1.1.529.2.75.3.4.1.1.1.1.1.7.1 |
| DV.7.2 | United Kingdom 91.0%, United States of America 3.0%, Canada 3.0%, France 3.0% | 2023-03-14 | 33 | 33 | Alias of B.1.1.529.2.75.3.4.1.1.1.1.1.7.2, C703T, England | NA | B.1.1.529.2.75.3.4.1.1.1.1.1.7.2 |
| DV.8 | Sweden 80.0%, Finland 5.0%, Norway 4.0%, Denmark 2.0%, United States of America 2.0% | 2023-01-07 | 164 | 197 | Alias of B.1.1.529.2.75.3.4.1.1.1.1.1.8, S:Q613H, C8299T, C19602T, Sweden | NA | B.1.1.529.2.75.3.4.1.1.1.1.1.8 |
| CH.1.1.2 | United Kingdom 42.0%, United States of America 10.0%, Germany 9.0%, Denmark 7.0%, Canada 6.0% | 2022-10-23 | 19 | 2264 | Alias of B.1.1.529.2.75.3.4.1.1.1.1.2, defined by S:T883I, ORF1a:Y1846C, ORF1a:G2294S on T27576C branch | NA | B.1.1.529.2.75.3.4.1.1.1.1.2 |
| CH.1.1.3 | New_Zealand 49.0%, Australia 19.0%, United Kingdom 7.0%, Germany 6.0%, Hong_Kong 4.0% | 2022-10-18 | 99 | 766 | Alias of B.1.1.529.2.75.3.4.1.1.1.1.3, S:S255P, New Zealand/Australia/Hong Kong, from #1405 | NA | B.1.1.529.2.75.3.4.1.1.1.1.3 |
| GQ.1 | Australia 59.0%, New_Zealand 26.0%, United States of America 4.0%, United Kingdom 4.0%, Canada 1.0% | 2023-02-24 | 32 | 68 | Alias of B.1.1.529.2.75.3.4.1.1.1.1.3.1, S:486P, ORF1a:H1545Q, ORF1b:V1520L, Australia/New Zealand, from #1872 | NA | B.1.1.529.2.75.3.4.1.1.1.1.3.1 |
| GQ.1.1 | New_Zealand 98.0%, Australia 2.0% | 2023-04-21 | 20 | 40 | Alias of B.1.1.529.2.75.3.4.1.1.1.1.3.1.1, S:G213E, New Zealand, from sars-cov-2-variants/lineage-proposals#343 | NA | B.1.1.529.2.75.3.4.1.1.1.1.3.1.1 |
| CH.1.1.5 | Denmark 61.0%, United Kingdom 26.0%, United States of America 4.0%, Sweden 4.0%, Slovenia 2.0% | 2022-11-09 | 82 | 391 | Alias of B.1.1.529.2.75.3.4.1.1.1.1.5, ORF3a:P104S, found mainly in Denmark and UK, from pango-designation issue #1539 | NA | B.1.1.529.2.75.3.4.1.1.1.1.5 |
| CH.1.1.6 | United Kingdom 91.0%, Ireland 2.0%, United States of America 1.0%, Luxembourg 1.0%, Spain 1.0% | 2022-11-15 | 122 | 495 | Alias of B.1.1.529.2.75.3.4.1.1.1.1.6, UK, defined by S:T732I | NA | B.1.1.529.2.75.3.4.1.1.1.1.6 |
| CH.1.1.7 | New_Zealand 52.0%, Australia 34.0%, United States of America 4.0%, Japan 4.0%, United Kingdom 1.0% | 2022-10-05 | 618 | 1325 | Alias of B.1.1.529.2.75.3.4.1.1.1.1.7, New Zealand/Australia, defined by ORF1a:F143C | NA | B.1.1.529.2.75.3.4.1.1.1.1.7 |
| CH.1.1.8 | United Kingdom 52.0%, Ireland 38.0%, Germany 3.0%, Denmark 2.0%, Switzerland 2.0% | 2022-11-05 | 99 | 329 | Alias of B.1.1.529.2.75.3.4.1.1.1.1.8, Ireland, defined by S:A846V | NA | B.1.1.529.2.75.3.4.1.1.1.1.8 |
| CH.1.1.9 | United Kingdom 92.0%, Germany 2.0%, United States of America 1.0%, Sweden 1.0%, Denmark 1.0% | 2022-11-15 | 128 | 214 | Alias of B.1.1.529.2.75.3.4.1.1.1.1.9, England, defined by S:I1232V | NA | B.1.1.529.2.75.3.4.1.1.1.1.9 |
| CH.1.1.10 | Ireland 41.0%, United Kingdom 38.0%, Netherlands 6.0%, Denmark 2.0%, Germany 2.0% | 2022-10-23 | 548 | 821 | Alias of B.1.1.529.2.75.3.4.1.1.1.1.10, Ireland, ORF1a:G442S | NA | B.1.1.529.2.75.3.4.1.1.1.1.10 |
| CH.1.1.11 | United Kingdom 12.0%, Australia 12.0%, Germany 11.0%, Japan 7.0%, Hong_Kong 7.0% | 2022-03-03 | 709 | 1548 | Alias of B.1.1.529.2.75.3.4.1.1.1.1.11, ORF1a:A1176T | NA | B.1.1.529.2.75.3.4.1.1.1.1.11 |
| GP.1 | Italy 31.0%, United Kingdom 20.0%, Ireland 9.0%, Australia 9.0%, Netherlands 6.0% | 2022-11-27 | 119 | 185 | Alias of B.1.1.529.2.75.3.4.1.1.1.1.11.1, S:Q52H, ORF7a:T28I, Europe | NA | B.1.1.529.2.75.3.4.1.1.1.1.11.1 |
| GP.2 | Germany 35.0%, United Kingdom 14.0%, Denmark 8.0%, Sweden 5.0%, Austria 5.0% | 2022-08-01 | 780 | 788 | Alias of B.1.1.529.2.75.3.4.1.1.1.1.11.2, ORF6:S41F, T13450C, Europe | NA | B.1.1.529.2.75.3.4.1.1.1.1.11.2 |
| GP.3 | Ireland 45.0%, United Kingdom 19.0%, France 6.0%, Germany 6.0%, Netherlands 5.0% | 2022-11-07 | 392 | 376 | Alias of B.1.1.529.2.75.3.4.1.1.1.1.11.3, T5218C, A16878G, A26519G, C29236T, Ireland | NA | B.1.1.529.2.75.3.4.1.1.1.1.11.3 |
| CH.1.1.12 | Denmark 84.0%, Austria 3.0%, Germany 3.0%, Sweden 3.0%, Netherlands 2.0% | 2022-11-25 | 202 | 618 | Alias of B.1.1.529.2.75.3.4.1.1.1.1.12, S:L858I on ORF1a:A486V branch, Denmark | NA | B.1.1.529.2.75.3.4.1.1.1.1.12 |
| FS.1 | Denmark 77.0%, Portugal 6.0%, France 4.0%, United Kingdom 3.0%, Sweden 2.0% | 2022-12-30 | 135 | 270 | Alias of B.1.1.529.2.75.3.4.1.1.1.1.12.1, found mainly in Denmark, from pango-designation issue #1816 | NA | B.1.1.529.2.75.3.4.1.1.1.1.12.1 |
| CH.1.1.13 | United Kingdom 91.0%, Denmark 3.0%, United States of America 1.0%, Norway 1.0%, Netherlands 1.0% | 2022-12-02 | 227 | 267 | Alias of B.1.1.529.2.75.3.4.1.1.1.1.13, ORF3a:S171L | NA | B.1.1.529.2.75.3.4.1.1.1.1.13 |
| CH.1.1.14 | United Kingdom 61.0%, Canada 7.0%, Belgium 6.0%, Germany 4.0%, United States of America 4.0% | 2022-10-19 | 125 | 267 | Alias of B.1.1.529.2.75.3.4.1.1.1.1.14, N:T362I | NA | B.1.1.529.2.75.3.4.1.1.1.1.14 |
| CH.1.1.15 | Lithuania 31.0%, Germany 24.0%, United Kingdom 19.0%, Denmark 4.0%, Norway 3.0% | 2022-11-24 | 159 | 557 | Alias of B.1.1.529.2.75.3.4.1.1.1.1.15, found mainly in Lithuania, Germany and UK, from pango-designation issue #1726 | NA | B.1.1.529.2.75.3.4.1.1.1.1.15 |
| CH.1.1.16 | Germany 31.0%, Sweden 30.0%, Denmark 7.0%, Austria 5.0%, United Kingdom 4.0% | 2022-12-07 | 83 | 322 | Alias of B.1.1.529.2.75.3.4.1.1.1.1.16, S:613H, ORF3a:S26L, on C193T branch, Germany/Sweden, from #1753 | NA | B.1.1.529.2.75.3.4.1.1.1.1.16 |
| CH.1.1.17 | Australia 45.0%, New_Zealand 23.0%, Solomon_Islands 14.0%, United Kingdom 9.0%, Papua_New_Guinea 6.0% | 2022-10-13 | 125 | 244 | Alias of B.1.1.529.2.75.3.4.1.1.1.1.17, M:S212G, on C21811T branch, from #1753 | NA | B.1.1.529.2.75.3.4.1.1.1.1.17 |
| FK.1 | New_Zealand 60.0%, Australia 22.0%, South_Korea 6.0%, United States of America 6.0%, Austria 1.0% | 2023-01-28 | 23 | 413 | Alias of B.1.1.529.2.75.3.4.1.1.1.1.17.1, found mainly in New Zealand and Australia, from pango-designation issue #1718 | NA | B.1.1.529.2.75.3.4.1.1.1.1.17.1 |
| FK.1.1 | New_Zealand 32.0%, Australia 29.0%, South_Korea 14.0%, United States of America 11.0%, Japan 6.0% | 2023-02-08 | 53 | 1210 | Alias of B.1.1.529.2.75.3.4.1.1.1.1.17.1.1, ORF1a:A1060T, on C27804T>ORF1b:L2580I>N:G34E branch, New Zealand, from #1881 | NA | B.1.1.529.2.75.3.4.1.1.1.1.17.1.1 |
| FK.1.1.1 | Australia 97.0%, New_Zealand 3.0% | 2023-04-23 | 21 | 33 | Alias of B.1.1.529.2.75.3.4.1.1.1.1.17.1.1.1, S:V445A, Australia From sars-cov-2-variants/lineage-proposals#368 | NA | B.1.1.529.2.75.3.4.1.1.1.1.17.1.1.1 |
| FK.1.1.2 | Australia 51.0%, New_Zealand 39.0%, Japan 3.0%, United States of America 3.0%, Canada 1.0% | 2023-03-04 | 726 | 757 | Alias of B.1.1.529.2.75.3.4.1.1.1.1.17.1.1.2, C9223T, T23071G | NA | B.1.1.529.2.75.3.4.1.1.1.1.17.1.1.2 |
| FK.1.2 | Slovenia 30.0%, New_Zealand 28.0%, Austria 20.0%, United Kingdom 10.0%, Denmark 3.0% | 2023-01-22 | 98 | 115 | Alias of B.1.1.529.2.75.3.4.1.1.1.1.17.1.2, ORF1a:L384F, ORF1a:R550H | NA | B.1.1.529.2.75.3.4.1.1.1.1.17.1.2 |
| FK.1.2.1 | Finland 32.0%, Denmark 28.0%, Germany 12.0%, Netherlands 8.0%, Austria 6.0% | 2023-02-04 | 174 | 251 | Alias of B.1.1.529.2.75.3.4.1.1.1.1.17.1.2.1, ORF1a:T891I, Germany/Denmark/Finland/Austria | NA | B.1.1.529.2.75.3.4.1.1.1.1.17.1.2.1 |
| FK.1.2.2 | New_Zealand 38.0%, Australia 22.0%, United States of America 19.0%, South_Korea 7.0%, Canada 6.0% | 2023-02-15 | 113 | 137 | Alias of B.1.1.529.2.75.3.4.1.1.1.1.17.1.2.2, ORF1a:D139N, ORF1a:R226K, ORF1a:Q556K, ORF3a:T64N, T11737C, AUS/NZ | NA | B.1.1.529.2.75.3.4.1.1.1.1.17.1.2.2 |
| FK.1.3 | Australia 75.0%, United States of America 22.0%, Sweden 1.0%, Japan 1.0% | 2023-02-18 | 24 | 67 | Alias of B.1.1.529.2.75.3.4.1.1.1.1.17.1.3, ORF1b:M1839I, on C27804T>ORF1b:L2580I>N:G34E branch, Australia | NA | B.1.1.529.2.75.3.4.1.1.1.1.17.1.3 |
| FK.1.3.1 | Australia 96.0%, United States of America 4.0% | 2023-02-20 | 54 | 57 | Alias of B.1.1.529.2.75.3.4.1.1.1.1.17.1.3.1, S:E583D, Australia | NA | B.1.1.529.2.75.3.4.1.1.1.1.17.1.3.1 |
| FK.1.3.2 | Japan 60.0%, Australia 32.0%, United States of America 3.0%, South_Korea 2.0%, Finland 1.0% | 2023-03-09 | 181 | 352 | Alias of B.1.1.529.2.75.3.4.1.1.1.1.17.1.3.2, C9391T, T13596C, Australia/Japan | NA | B.1.1.529.2.75.3.4.1.1.1.1.17.1.3.2 |
| FK.1.4 | Australia 100.0% | 2023-02-01 | 49 | 130 | Alias of B.1.1.529.2.75.3.4.1.1.1.1.17.1.4, S:S704L, on C27804>ORF7a:Y40H branch, Australia | NA | B.1.1.529.2.75.3.4.1.1.1.1.17.1.4 |
| FK.1.4.1 | Australia 81.0%, Puerto_Rico 12.0%, United States of America 6.0% | 2023-04-01 | 34 | 32 | Alias of B.1.1.529.2.75.3.4.1.1.1.1.17.1.4.1, S:G181A, Australia/Puerto Rico From sars-cov-2-variants/lineage-proposals#88 | NA | B.1.1.529.2.75.3.4.1.1.1.1.17.1.4.1 |
| FK.1.5 | Australia 53.0%, New_Zealand 15.0%, United States of America 14.0%, Canada 10.0%, Sweden 4.0% | 2023-02-20 | 205 | 227 | Alias of B.1.1.529.2.75.3.4.1.1.1.1.17.1.5, G5155A, C12439T, Australia/New Zealand | NA | B.1.1.529.2.75.3.4.1.1.1.1.17.1.5 |
| CH.1.1.18 | United Kingdom 28.0%, United States of America 23.0%, Germany 17.0%, Austria 6.0%, India 5.0% | 2022-10-03 | 173 | 248 | Alias of B.1.1.529.2.75.3.4.1.1.1.1.18, S:K187T, related to #1747 | NA | B.1.1.529.2.75.3.4.1.1.1.1.18 |
Creating a PangoRo object
Most of the functions refer to a designated object (S3) in R. This allows one to specify how one wants to operate with the alias conversions. For instance, the object can be created to be in an ‘offline’ mode.
alias lineage
1 A
2 B
3 C B.1.1.1
4 D B.1.1.25
5 G B.1.258.2
6 K B.1.1.277
7 L B.1.1.10
8 M B.1.1.294
9 N B.1.1.33
10 P B.1.1.28
11 Q B.1.1.7
12 R B.1.1.316
13 S B.1.1.217
14 U B.1.177.60
15 V B.1.177.54
16 W B.1.177.53
17 Y B.1.177.52
18 Z B.1.177.50
19 AA B.1.177.15
20 AB B.1.160.16
21 AC B.1.1.405
22 AD B.1.1.315
23 AE B.1.1.306
24 AF B.1.1.305
25 AG B.1.1.297
26 AH B.1.1.241
27 AJ B.1.1.240
28 AK B.1.1.232
29 AL B.1.1.231
30 AM B.1.1.216
31 AN B.1.1.200
32 AP B.1.1.70
33 AQ B.1.1.39
34 AS B.1.1.317
35 AT B.1.1.370
36 AU B.1.466.2
37 AV B.1.1.482
38 AW B.1.1.464
39 AY B.1.617.2
40 AZ B.1.1.318
41 BA B.1.1.529
42 BB B.1.621.1
43 BC B.1.1.529.1.1.1
44 BD B.1.1.529.1.17.2
45 BE B.1.1.529.5.3.1
46 BF B.1.1.529.5.2.1
47 BG B.1.1.529.2.12.1
48 BH B.1.1.529.2.38.3
49 BJ B.1.1.529.2.10.1
50 BK B.1.1.529.5.1.10
51 BL B.1.1.529.2.75.1
52 BM B.1.1.529.2.75.3
53 BN B.1.1.529.2.75.5
54 BP B.1.1.529.2.3.16
55 BQ B.1.1.529.5.3.1.1.1.1
56 BR B.1.1.529.2.75.4
57 BS B.1.1.529.2.3.2
58 BT B.1.1.529.5.1.21
59 BU B.1.1.529.5.2.16
60 BV B.1.1.529.5.2.20
61 BW B.1.1.529.5.6.2
62 BY B.1.1.529.2.75.6
63 BZ B.1.1.529.5.2.3
64 CA B.1.1.529.2.75.2
65 CB B.1.1.529.2.75.9
66 CC B.1.1.529.5.3.1.1.1.2
67 CD B.1.1.529.5.2.31
68 CE B.1.1.529.5.2.33
69 CF B.1.1.529.5.2.27
70 CG B.1.1.529.5.2.26
71 CH B.1.1.529.2.75.3.4.1.1
72 CJ B.1.1.529.2.75.3.1.1.1
73 CK B.1.1.529.5.2.24
74 CL B.1.1.529.5.1.29
75 CM B.1.1.529.2.3.20
76 CN B.1.1.529.5.2.21
77 CP B.1.1.529.5.2.6
78 CQ B.1.1.529.5.3.1.4.1.1
79 CR B.1.1.529.5.2.18
80 CS B.1.1.529.4.1.10
81 CT B.1.1.529.5.2.36
82 CU B.1.1.529.5.1.26
83 CV B.1.1.529.2.75.3.1.1.3
84 CW B.1.1.529.5.3.1.1.1.1.1.1.14
85 CY B.1.1.529.5.2.7
86 CZ B.1.1.529.5.3.1.1.1.1.1.1.1
87 DA B.1.1.529.5.2.38
88 DB B.1.1.529.5.2.25
89 DC B.1.1.529.4.6.5
90 DD B.1.1.529.2.3.21
91 DE B.1.1.529.5.1.23
92 DF B.1.1.529.5.10.1
93 DG B.1.1.529.5.2.24.2.1.1
94 DH B.1.1.529.5.1.22
95 DJ B.1.1.529.5.1.25
96 DK B.1.1.529.5.3.1.1.1.1.1.1.7
97 DL B.1.1.529.5.1.15
98 DM B.1.1.529.5.3.1.1.1.1.1.1.15
99 DN B.1.1.529.5.3.1.1.1.1.1.1.5
100 DP B.1.1.529.5.3.1.1.1.1.1.1.8
101 DQ B.1.1.529.5.2.47
102 DR B.1.1.529.5.3.1.1.1.1.1.1.3
103 DS B.1.1.529.2.75.5.1.3.1
104 DT B.1.1.529.5.3.1.1.1.1.1.1.32
105 DU B.1.1.529.5.3.1.1.1.1.1.1.2
106 DV B.1.1.529.2.75.3.4.1.1.1.1.1
107 DW B.1.1.529.5.3.1.1.2.1
108 DY B.1.1.529.5.2.48
109 DZ B.1.1.529.5.2.49
110 EA B.1.1.529.5.3.1.1.1.1.1.1.52
111 EB B.1.1.529.5.1.35
112 EC B.1.1.529.5.3.1.1.1.1.1.10.1
113 ED B.1.1.529.5.3.1.1.1.1.1.1.18
114 EE B.1.1.529.5.3.1.1.1.1.1.1.4
115 EF B.1.1.529.5.3.1.1.1.1.1.1.13
116 EG XBB.1.9.2
117 EH B.1.1.529.5.3.1.1.1.1.1.1.28
118 EJ B.1.1.529.2.75.5.1.3.8
119 EK XBB.1.5.13
120 EL XBB.1.5.14
121 EM XBB.1.5.7
122 EN B.1.1.529.5.3.1.1.1.1.1.1.46
123 EP B.1.1.529.2.75.3.1.1.4
124 EQ B.1.1.529.5.1.33
125 ER B.1.1.529.5.3.1.1.1.1.1.1.22
126 ES B.1.1.529.5.3.1.1.1.1.1.1.65
127 ET B.1.1.529.5.3.1.1.1.1.1.1.35
128 EU XBB.1.5.26
129 EV B.1.1.529.5.3.1.1.1.1.1.1.71
130 EW B.1.1.529.5.3.1.1.1.1.1.1.38
131 EY B.1.1.529.5.3.1.1.1.1.1.1.13.1.1.1
132 EZ B.1.1.529.5.3.1.1.1.1.1.1.43
133 FA B.1.1.529.5.3.1.1.1.1.1.1.10
134 FB B.1.1.529.5.3.1.1.1.1.1.2.1
135 FC B.1.1.529.5.3.1.1.1.1.1.1.72
136 FD XBB.1.5.15
137 FE XBB.1.18.1
138 FF B.1.1.529.5.3.1.1.1.1.1.8.2
139 FG XBB.1.5.16
140 FH XBB.1.5.17
141 FJ B.1.1.529.2.75.3.4.1.1.1.1.19
142 FK B.1.1.529.2.75.3.4.1.1.1.1.17
143 FL XBB.1.9.1
144 FM B.1.1.529.5.3.1.1.1.1.1.1.53
145 FN B.1.1.529.5.3.1.1.1.1.1.1.74
146 FP XBB.1.11.1
147 FQ B.1.1.529.5.3.1.1.1.1.1.1.39
148 FR B.1.1.529.2.75.5.1.2.3
149 FS B.1.1.529.2.75.3.4.1.1.1.1.12
150 FT XBB.1.5.39
151 FU XBB.1.16.1
152 FV B.1.1.529.2.3.20.8.1.1
153 FW XBB.1.28.1
154 FY XBB.1.22.1
155 FZ XBB.1.5.47
156 GA XBB.1.17.1
157 GB XBB.1.5.46
158 GC XBB.1.5.21
159 GD XBB.1.9.3
160 GE XBB.2.3.10
161 GF XBB.1.5.24
162 GG XBB.1.5.38
163 GH XBB.2.6.1
164 GJ XBB.2.3.3
165 GK XBB.1.5.70
166 GL XAY.1.1.1
167 GM XBB.2.3.6
168 GN XBB.1.5.73
169 GP B.1.1.529.2.75.3.4.1.1.1.1.11
170 GQ B.1.1.529.2.75.3.4.1.1.1.1.3
171 GR XBB.1.5.42
172 GS XBB.2.3.11
173 GT XBC.1.6.1
174 GU XBB.1.5.41
175 GV XBB.1.5.48
176 GW XBB.1.19.1
177 GY XBB.1.16.2
178 GZ XBB.2.3.4
179 HA XBB.1.5.86
180 HB XBB.1.34.2
181 HC XBB.1.5.44
182 HD XBB.1.5.93
183 HE XBB.1.18.1.1.1.1
184 HF XBB.1.16.13
185 HG XBB.2.3.8
186 HH XBB.2.3.2
187 HJ XBB.1.5.1
188 HK XBB.1.9.2.5.1.1
189 HL XBB.1.42.2
190 HM XBB.1.5.30
191 HN XBB.1.9.1.1.5.1
192 HP XBB.1.5.55
193 HQ XBB.1.5.92
194 HR XBB.1.5.77
195 HS XBB.1.5.95
196 HT XBB.1.5.49
197 HU XBB.1.22.2
198 HV XBB.1.9.2.5.1.6
199 HW XBC.1.6.3
200 HY XBB.1.5.100
201 HZ XBB.1.5.68
202 JA XBB.2.3.13
203 JB XBB.1.5.53
204 JC XBB.1.41.1
205 JD XBB.1.5.102
206 JE XBB.2.3.3.1.2.1
207 JF XBB.1.16.6
208 XA B.1.1.7
209 XA B.1.177
210 XB B.1.634
211 XB B.1.631
212 XC AY.29
213 XC B.1.1.7
214 XD B.1.617.2
215 XD BA.1
216 XE BA.1
217 XE BA.2
218 XF B.1.617.2
219 XF BA.1
220 XG BA.1
221 XG BA.2
222 XH BA.1
223 XH BA.2
224 XJ BA.1
225 XJ BA.2
226 XK BA.1
227 XK BA.2
228 XL BA.1
229 XL BA.2
230 XM BA.1.1
231 XM BA.2
232 XN BA.1
233 XN BA.2
234 XP BA.1.1
235 XP BA.2
236 XQ BA.1.1
237 XQ BA.2
238 XR BA.1.1
239 XR BA.2
240 XS B.1.617.2
241 XS BA.1.1
242 XT BA.2
243 XT BA.1
244 XU BA.1
245 XU BA.2
246 XV BA.1
247 XV BA.2
248 XW BA.1
249 XW BA.2
250 XY BA.1
251 XY BA.2
252 XZ BA.2
253 XZ BA.1
254 XAA BA.1
255 XAA BA.2
256 XAB BA.1
257 XAB BA.2
258 XAC BA.2
259 XAC BA.1
260 XAC BA.2
261 XAD BA.2
262 XAD BA.1
263 XAE BA.2
264 XAE BA.1
265 XAF BA.1
266 XAF BA.2
267 XAG BA.1
268 XAG BA.2
269 XAH BA.2
270 XAH BA.1
271 XAJ BA.2.12.1
272 XAJ BA.4
273 XAK BA.2
274 XAK BA.1
275 XAK BA.2
276 XAL BA.1
277 XAL BA.2
278 XAM BA.1.1
279 XAM BA.2.9
280 XAN BA.2
281 XAN BA.5.1
282 XAP BA.2
283 XAP BA.1
284 XAQ BA.1
285 XAQ BA.2
286 XAR BA.1
287 XAR BA.2
288 XAS BA.5
289 XAS BA.2
290 XAT BA.2.3.13
291 XAT BA.1
292 XAU BA.1.1
293 XAU BA.2.9
294 XAV BA.2
295 XAV BA.5
296 XAW BA.2
297 XAW AY.122
298 XAY BA.2
299 XAY AY.45
300 XAY BA.2
301 XAY AY.45
302 XAY BA.2
303 XAZ BA.2.5
304 XAZ BA.5
305 XAZ BA.2.5
306 XBA BA.2
307 XBA AY.45
308 XBA BA.2
309 XBA AY.45
310 XBA BA.2
311 XBB BJ.1
312 XBB BM.1.1.1
313 XBC BA.2
314 XBC B.1.617.2
315 XBC BA.2
316 XBC B.1.617.2
317 XBD BA.2.75.2
318 XBD BF.5
319 XBE BA.5.2
320 XBE BE.4.1
321 XBF BA.5.2.3
322 XBF CJ.1
323 XBG BA.2.76
324 XBG BA.5.2
325 XBH BA.2.3.17
326 XBH BA.2.75.2
327 XBJ BA.2.3.20
328 XBJ BA.5.2
329 XBK BA.5.2
330 XBK CJ.1
331 XBL XBB.1.5.57
332 XBL BA.2.75
333 XBL XBB.1.5.57
334 XBM BA.2.76
335 XBM BF.3
336 XBN BA.2.75
337 XBN XBB.3
338 XBP BA.2.75
339 XBP BQ.1
340 XBQ BA.5.2
341 XBQ CJ.1
342 XBR BA.2.75
343 XBR BQ.1
344 XBS BA.2.75
345 XBS BQ.1
346 XBT BA.5.2.34
347 XBT BA.2.75
348 XBT BA.5.2.34
349 XBU BA.2.75.3
350 XBU BQ.1
351 XBU BA.2.75.3
352 XBV CR.1
353 XBV XBB.1
354 XBW XBB.1.5
355 XBW BQ.1.14
356 XBY BR.2.1
357 XBY XBF
358 XBZ BA.5.2
359 XBZ EF.1.3
360 XCA BA.2.75
361 XCA BQ.1
362 XCB BF.31.1
363 XCB BQ.1.10
364 XCC CH.1.1.1
365 XCC XBB.1.9.1
366 XCD XBB.1
367 XCD BQ.1.1.25
368 XCE BQ.1
369 XCE FY.1
370 XCF XBB
371 XCF FE.1
372 XCG BA.5.2
373 XCG XBB.1
374 XCH GK.1.3
375 XCH XBB.1.9
376 XCH GK.1.3
377 XCJ GM.2
378 XCJ FP.1
379 XCJ GM.2Basic Commands: Expand & Collapse
BA.1 B.1.1.529.1
BM.1 B.1.1.529.2.75.3.1Basic Commands: Sort
Take lineage list and place in semi-sorted order.
# Perform linear sort
sorted_lin <- sort_pangoro(my_pangoro,
c('BL.1', 'BA.1', 'BM.1', 'BQ.3'))
# Examine sort after expanded from aliases
expand_pangoro(my_pangoro, sorted_lin) |>
data.frame(fix.empty.names = FALSE)
BA.1 B.1.1.529.1
BL.1 B.1.1.529.2.75.1.1
BM.1 B.1.1.529.2.75.3.1
BQ.3 B.1.1.529.5.3.1.1.1.1.3Basic Commands: Search
Examine if BL.1 is a child or parent of BA.2.
Advanced Use: Programmatic Look Ups
Group lineage list into:
- BA.2
- Recombinant
- Other
Dummy Data-set
| COVID-19 Lineages | N |
|---|---|
| AY | 1 |
| B.1.1.529.1.1 | 14 |
| B.1.1.529.2 | 5 |
| B.1.617.2 | 2 |
| BE | 15 |
| BL | 13 |
| BQ | 7 |
| CC | 11 |
| EF | 8 |
| XAY | 6 |
| XBB | 9 |
Advanced Use Continued…
Examine lineages and expand aliases from covid_lineages data set.
B.1.617.2 B.1.1.529.2
"B.1.617.2" "B.1.1.529.2"
BE BL
"B.1.1.529.5.3.1" "B.1.1.529.2.75.1"
BQ CC
"B.1.1.529.5.3.1.1.1.1" "B.1.1.529.5.3.1.1.1.2"
AY EF
"B.1.617.2" "B.1.1.529.5.3.1.1.1.1.1.1.13"
XBB XAY
"XBB" "XAY"
B.1.1.529.1.1
"B.1.1.529.1.1" Advanced Use Continued…
Create look-up based on index matching in searches.
# Create index for groups
index_match_ba2 <- mapply('BA.2', unique(covid_lineages),
FUN = \(x, y) search_pangoro(my_pangoro, x, y),
USE.NAMES = FALSE)
index_match_recom <- startsWith(exp_lin, 'X')
# Create initial data set
lineage_lu <- data.frame(Grouping = 'Other',
Source = unique(covid_lineages),
Expanded = exp_lin, row.names = NULL)
# Overwite using index with groupings
lineage_lu[index_match_ba2, 'Grouping'] <- 'BA.2'
lineage_lu[index_match_recom, 'Grouping'] <- 'Recombinant'
lineage_lu |>
knitr::kable(table.attr = "style=\"width: 100%\"") |>
kableExtra::scroll_box() |>
kableExtra::kable_styling(font_size = 20,
bootstrap_options = 'striped',
fixed_thead = list(enabled = TRUE,
background = 'black'))Advanced Use Continued…
| Grouping | Source | Expanded |
|---|---|---|
| Other | B.1.617.2 | B.1.617.2 |
| BA.2 | B.1.1.529.2 | B.1.1.529.2 |
| Other | BE | B.1.1.529.5.3.1 |
| BA.2 | BL | B.1.1.529.2.75.1 |
| Other | BQ | B.1.1.529.5.3.1.1.1.1 |
| Other | CC | B.1.1.529.5.3.1.1.1.2 |
| Other | AY | B.1.617.2 |
| Other | EF | B.1.1.529.5.3.1.1.1.1.1.1.13 |
| Recombinant | XBB | XBB |
| Recombinant | XAY | XAY |
| Other | B.1.1.529.1.1 | B.1.1.529.1.1 |
Advanced Use Continued…
Merge back to original data set.
merge(data.frame(lineage = covid_lineages),
lineage_lu,
by.x = 'lineage', by.y = 'Source') |>
knitr::kable(table.attr = "style=\"width: 100%\"") |>
kableExtra::scroll_box(height = '300px') |>
kableExtra::kable_styling(font_size = 20,
bootstrap_options = 'striped',
fixed_thead = list(enabled = TRUE,
background = 'black'))| lineage | Grouping | Expanded |
|---|---|---|
| AY | Other | B.1.617.2 |
| B.1.1.529.1.1 | Other | B.1.1.529.1.1 |
| B.1.1.529.1.1 | Other | B.1.1.529.1.1 |
| B.1.1.529.1.1 | Other | B.1.1.529.1.1 |
| B.1.1.529.1.1 | Other | B.1.1.529.1.1 |
| B.1.1.529.1.1 | Other | B.1.1.529.1.1 |
| B.1.1.529.1.1 | Other | B.1.1.529.1.1 |
| B.1.1.529.1.1 | Other | B.1.1.529.1.1 |
| B.1.1.529.1.1 | Other | B.1.1.529.1.1 |
| B.1.1.529.1.1 | Other | B.1.1.529.1.1 |
| B.1.1.529.1.1 | Other | B.1.1.529.1.1 |
| B.1.1.529.1.1 | Other | B.1.1.529.1.1 |
| B.1.1.529.1.1 | Other | B.1.1.529.1.1 |
| B.1.1.529.1.1 | Other | B.1.1.529.1.1 |
| B.1.1.529.1.1 | Other | B.1.1.529.1.1 |
| B.1.1.529.2 | BA.2 | B.1.1.529.2 |
| B.1.1.529.2 | BA.2 | B.1.1.529.2 |
| B.1.1.529.2 | BA.2 | B.1.1.529.2 |
| B.1.1.529.2 | BA.2 | B.1.1.529.2 |
| B.1.1.529.2 | BA.2 | B.1.1.529.2 |
| B.1.617.2 | Other | B.1.617.2 |
| B.1.617.2 | Other | B.1.617.2 |
| BE | Other | B.1.1.529.5.3.1 |
| BE | Other | B.1.1.529.5.3.1 |
| BE | Other | B.1.1.529.5.3.1 |
| BE | Other | B.1.1.529.5.3.1 |
| BE | Other | B.1.1.529.5.3.1 |
| BE | Other | B.1.1.529.5.3.1 |
| BE | Other | B.1.1.529.5.3.1 |
| BE | Other | B.1.1.529.5.3.1 |
| BE | Other | B.1.1.529.5.3.1 |
| BE | Other | B.1.1.529.5.3.1 |
| BE | Other | B.1.1.529.5.3.1 |
| BE | Other | B.1.1.529.5.3.1 |
| BE | Other | B.1.1.529.5.3.1 |
| BE | Other | B.1.1.529.5.3.1 |
| BE | Other | B.1.1.529.5.3.1 |
| BL | BA.2 | B.1.1.529.2.75.1 |
| BL | BA.2 | B.1.1.529.2.75.1 |
| BL | BA.2 | B.1.1.529.2.75.1 |
| BL | BA.2 | B.1.1.529.2.75.1 |
| BL | BA.2 | B.1.1.529.2.75.1 |
| BL | BA.2 | B.1.1.529.2.75.1 |
| BL | BA.2 | B.1.1.529.2.75.1 |
| BL | BA.2 | B.1.1.529.2.75.1 |
| BL | BA.2 | B.1.1.529.2.75.1 |
| BL | BA.2 | B.1.1.529.2.75.1 |
| BL | BA.2 | B.1.1.529.2.75.1 |
| BL | BA.2 | B.1.1.529.2.75.1 |
| BL | BA.2 | B.1.1.529.2.75.1 |
| BQ | Other | B.1.1.529.5.3.1.1.1.1 |
| BQ | Other | B.1.1.529.5.3.1.1.1.1 |
| BQ | Other | B.1.1.529.5.3.1.1.1.1 |
| BQ | Other | B.1.1.529.5.3.1.1.1.1 |
| BQ | Other | B.1.1.529.5.3.1.1.1.1 |
| BQ | Other | B.1.1.529.5.3.1.1.1.1 |
| BQ | Other | B.1.1.529.5.3.1.1.1.1 |
| CC | Other | B.1.1.529.5.3.1.1.1.2 |
| CC | Other | B.1.1.529.5.3.1.1.1.2 |
| CC | Other | B.1.1.529.5.3.1.1.1.2 |
| CC | Other | B.1.1.529.5.3.1.1.1.2 |
| CC | Other | B.1.1.529.5.3.1.1.1.2 |
| CC | Other | B.1.1.529.5.3.1.1.1.2 |
| CC | Other | B.1.1.529.5.3.1.1.1.2 |
| CC | Other | B.1.1.529.5.3.1.1.1.2 |
| CC | Other | B.1.1.529.5.3.1.1.1.2 |
| CC | Other | B.1.1.529.5.3.1.1.1.2 |
| CC | Other | B.1.1.529.5.3.1.1.1.2 |
| EF | Other | B.1.1.529.5.3.1.1.1.1.1.1.13 |
| EF | Other | B.1.1.529.5.3.1.1.1.1.1.1.13 |
| EF | Other | B.1.1.529.5.3.1.1.1.1.1.1.13 |
| EF | Other | B.1.1.529.5.3.1.1.1.1.1.1.13 |
| EF | Other | B.1.1.529.5.3.1.1.1.1.1.1.13 |
| EF | Other | B.1.1.529.5.3.1.1.1.1.1.1.13 |
| EF | Other | B.1.1.529.5.3.1.1.1.1.1.1.13 |
| EF | Other | B.1.1.529.5.3.1.1.1.1.1.1.13 |
| XAY | Recombinant | XAY |
| XAY | Recombinant | XAY |
| XAY | Recombinant | XAY |
| XAY | Recombinant | XAY |
| XAY | Recombinant | XAY |
| XAY | Recombinant | XAY |
| XBB | Recombinant | XBB |
| XBB | Recombinant | XBB |
| XBB | Recombinant | XBB |
| XBB | Recombinant | XBB |
| XBB | Recombinant | XBB |
| XBB | Recombinant | XBB |
| XBB | Recombinant | XBB |
| XBB | Recombinant | XBB |
| XBB | Recombinant | XBB |